:: DESCRIPTION
UTGB Toolkit (University of Tokyo Genome Browser) is an open-source software for developing personalized genome browsers that work in web browsers.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Aug 1;25(15):1856-61. Epub 2009 Jun 3.
UTGB toolkit for personalized genome browsers.
Saito TL, Yoshimura J, Sasaki S, Ahsan B, Sasaki A, Kuroshu R, Morishita S.
:: DESCRIPTION
SMRT® View is an open source Genome Browser that visualizes data generated by PacBio® Sequencing Systems.
::DEVELOPER
Pacific Biosciences of California, Inc
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
CRAMER is a customisable, JavaScript and Jade based genome browser for interactive exploration of genomic data. Data is visualized in the browser, meaning CRAMER can be installed on any website and show data from a wide range of online, ftp links or local sources. CRAMER works with a variety of formats, such as XML, JSON, BED, VCF, GFF, GFF3, BAM or delimited text files, and can be customised to parse and display any data source as required.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Anastasiadi M, Bragin E, Biojoux P, Ahamed A, Burgin J, de Castro Cogle K, Llaneza-Lago S, Muvunyi R, Scislak M, Aktan I, Molitor C, Kurowski T, Mohareb F.
CRAMER: a lightweight, highly customizable web-based genome browser supporting multiple visualization instances.
Bioinformatics. 2020 Jun 1;36(11):3556-3557. doi: 10.1093/bioinformatics/btaa146. PMID: 32108858.
:: DESCRIPTION
iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser
::DEVELOPER
: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
“iPiG: Integrating Peptide Spectrum Matches Into Genome Browser Visualizations”
Mathias Kuhring and Bernhard Y. Renard
PLoS ONE 7(12): e50246. doi:10.1371/journal.pone.0050246
:: DESCRIPTION
ChromoZoom is a web-based genome browser currently hosting tracks for the yeast and human genomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Feb 1;29(3):384-6. doi: 10.1093/bioinformatics/bts695. Epub 2012 Dec 6.
ChromoZoom: a flexible, fluid, web-based genome browser.
Pak TR, Roth FP.
:: DESCRIPTION
RNASeqBrowser is a visualization tool that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs, InDels and raw read tracks with other BED and wiggle tracks — all being dynamically built from the BAM file.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The rtracklayer package supports the integration of existing genome browsers with experimental data analyses performed in R.
:: DEVELOPER
Michael Lawrence <michafla@gene.com>, Vincent J Carey, Robert Gentleman
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2009 Jul 15;25(14):1841-2. doi: 10.1093/bioinformatics/btp328..
rtracklayer: an R package for interfacing with genome browsers.
Lawrence M, Gentleman R, Carey V.
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:: DESCRIPTION
Rgb (R genome browser) package is dedicated to memory efficient genome browsing strategies (both in scripts and interactive sessions) using the R scripting language. It includes classes and functions to manipulate genomic tracks, and a higher level interactive genome browser.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Apr 21.
Rgb: a scriptable genome browser for R.
Mareschal S1, Dubois S, Lecroq T, Jardin F.
:: DESCRIPTION
JBrowse is a JavaScript genome browser with an emphasis on portability. JBrowse helps preserve the user’s sense of location by avoiding discontinuous transitions, instead offering smoothly animated panning, zooming, navigation, and track selection. Unlike most existing genome browsers, where the genome is rendered into images on the webserver and the role of the client is restricted to displaying those images, JBrowse distributes work between the server and client and therefore uses significantly less server overhead than previous genome browsers.
::DEVELOPER
Holmes lab at UC Berkeley
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
JBrowse: a next-generation genome browser.
Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH.
Genome Res. 2009 Sep;19(9):1630-8. doi: 10.1101/gr.094607.109
:: DESCRIPTION
cis-Browser (cis-Regulatory Browser) is genome browser for cis-regulatory information inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation
::DEVELOPER
The Istrail Laboratory of Brown University
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Mol Biol. 2010;674:369-99. doi: 10.1007/978-1-60761-854-6_22.
Practical computational methods for regulatory genomics: a cisGRN-Lexicon and cisGRN-browser for gene regulatory networks.
Istrail S, Tarpine R, Schutter K, Aguiar D.
